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Ferdoush J, Kadir RA, Ogle M, Saha A. Regulation of eukaryotic transcription initiation in response to cellular stress. Gene 2024; 924:148616. [PMID: 38795856 DOI: 10.1016/j.gene.2024.148616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 05/17/2024] [Accepted: 05/22/2024] [Indexed: 05/28/2024]
Abstract
Transcription initiation is a vital step in the regulation of eukaryotic gene expression. It can be dysregulated in response to various cellular stressors which is associated with numerous human diseases including cancer. Transcription initiation is facilitated via many gene-specific trans-regulatory elements such as transcription factors, activators, and coactivators through their interactions with transcription pre-initiation complex (PIC). These trans-regulatory elements can uniquely facilitate PIC formation (hence, transcription initiation) in response to cellular nutrient stress. Cellular nutrient stress also regulates the activity of other pathways such as target of rapamycin (TOR) pathway. TOR pathway exhibits distinct regulatory mechanisms of transcriptional activation in response to stress. Like TOR pathway, the cell cycle regulatory pathway is also found to be linked to transcriptional regulation in response to cellular stress. Several transcription factors such as p53, C/EBP Homologous Protein (CHOP), activating transcription factor 6 (ATF6α), E2F, transforming growth factor (TGF)-β, Adenomatous polyposis coli (APC), SMAD, and MYC have been implicated in regulation of transcription of target genes involved in cell cycle progression, apoptosis, and DNA damage repair pathways. Additionally, cellular metabolic and oxidative stressors have been found to regulate the activity of long non-coding RNAs (lncRNA). LncRNA regulates transcription by upregulating or downregulating the transcription regulatory proteins involved in metabolic and cell signaling pathways. Numerous human diseases, triggered by chronic cellular stressors, are associated with abnormal regulation of transcription. Hence, understanding these mechanisms would help unravel the molecular regulatory insights with potential therapeutic interventions. Therefore, here we emphasize the recent advances of regulation of eukaryotic transcription initiation in response to cellular stress.
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Affiliation(s)
- Jannatul Ferdoush
- Department of Biology, Geology, and Environmental Science, University of Tennessee at Chattanooga, 615 McCallie Ave, Chattanooga, TN 37403, USA.
| | - Rizwaan Abdul Kadir
- Department of Biology, Geology, and Environmental Science, University of Tennessee at Chattanooga, 615 McCallie Ave, Chattanooga, TN 37403, USA
| | - Matthew Ogle
- Department of Biology, Geology, and Environmental Science, University of Tennessee at Chattanooga, 615 McCallie Ave, Chattanooga, TN 37403, USA
| | - Ayan Saha
- Department of Bioinformatics and Biotechnology, Asian University for Women, Chattogram, Bangladesh
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2
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Cooper SL, Lucius AL, Schneider DA. Quantifying the impact of initial RNA primer length on nucleotide addition by RNA polymerase I. Biophys Chem 2024; 305:107151. [PMID: 38088007 DOI: 10.1016/j.bpc.2023.107151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/30/2023] [Accepted: 12/04/2023] [Indexed: 01/03/2024]
Abstract
Transient state kinetic studies of eukaryotic DNA-dependent RNA polymerases (Pols) in vitro provide quantitative characterization of enzyme activity at the level of individual nucleotide addition events. Previous work revealed heterogeneity in the rate constants governing nucleotide addition by yeast RNA polymerase I (Pol I) for each position on a template DNA. In contrast, the rate constants that described nucleotide addition by yeast RNA polymerase II (Pol II) were more homogeneous. This observation led to the question, what drives the variability of rate constants governing RNA synthesis by Pol I? Are the kinetics of nucleotide addition dictated by the position of the nascent RNA within the polymerase or by the identity of the next encoded nucleotide? In this study, we examine the impact of nucleotide position (i.e. nascent RNA primer length) on the rate constants governing nine sequential nucleotide addition events catalyzed by Pol I. The results reveal a conserved trend in the observed rate constants at each position for all primer lengths used, and highlight that the 9-nucleotide, or 9-mer, RNA primer provides the fastest observed rate constants. These findings suggest that the observed heterogeneity of rate constants for RNA synthesis by Pol I in vitro is driven primarily by the template sequence.
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Affiliation(s)
- Stephanie L Cooper
- Department of Biochemistry and Molecular Genetics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Aaron L Lucius
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
| | - David A Schneider
- Department of Biochemistry and Molecular Genetics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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3
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Calil Brondani J, Afful D, Nune H, Hart J, Cook S, Momany C. Overproduction, purification, and transcriptional activity of recombinant Acinetobacter baylyi ADP1 RNA polymerase holoenzyme. Protein Expr Purif 2023; 206:106254. [PMID: 36804950 DOI: 10.1016/j.pep.2023.106254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/14/2023] [Accepted: 02/15/2023] [Indexed: 02/19/2023]
Abstract
Acinetobacter baylyi is an interesting model organism to investigate bacterial metabolism due to its vast repertoire of metabolic enzymes and ease of genetic manipulation. However, the study of gene expression in vitro is dependent on the availability of its RNA polymerase (RNAp), an essential enzyme in transcription. In this work, we developed a convenient method of producing the recombinant A. baylyi ADP1 RNA polymerase holoenzyme (RNApholo) in E. coli that yields 22 mg of a >96% purity protein from a 1-liter shake flask culture. We further characterized the A. baylyi ADP1 RNApholo kinetic profile using T7 Phage DNA as template and demonstrated that it is a highly transcriptionally active enzyme with an elongation rate of 24 nt/s and a termination efficiency of 94%. Moreover, the A. baylyi ADP1 RNApholo has a substantial sequence identity (∼95%) with the RNApholo from the human pathogen Acinetobacter baumannii. This protein can serve as a source of material for structural and biological studies towards advancing our understanding of genome expression and regulation in Acinetobacter species.
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Affiliation(s)
- Juliana Calil Brondani
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Derrick Afful
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Hanna Nune
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Jesse Hart
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Shelby Cook
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Cory Momany
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA, 30602, USA.
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4
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Wee LM, Tong AB, Florez Ariza AJ, Cañari-Chumpitaz C, Grob P, Nogales E, Bustamante CJ. A trailing ribosome speeds up RNA polymerase at the expense of transcript fidelity via force and allostery. Cell 2023; 186:1244-1262.e34. [PMID: 36931247 PMCID: PMC10135430 DOI: 10.1016/j.cell.2023.02.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 11/14/2022] [Accepted: 02/06/2023] [Indexed: 03/18/2023]
Abstract
In prokaryotes, translation can occur on mRNA that is being transcribed in a process called coupling. How the ribosome affects the RNA polymerase (RNAP) during coupling is not well understood. Here, we reconstituted the E. coli coupling system and demonstrated that the ribosome can prevent pausing and termination of RNAP and double the overall transcription rate at the expense of fidelity. Moreover, we monitored single RNAPs coupled to ribosomes and show that coupling increases the pause-free velocity of the polymerase and that a mechanical assisting force is sufficient to explain the majority of the effects of coupling. Also, by cryo-EM, we observed that RNAPs with a terminal mismatch adopt a backtracked conformation, while a coupled ribosome allosterically induces these polymerases toward a catalytically active anti-swiveled state. Finally, we demonstrate that prolonged RNAP pausing is detrimental to cell viability, which could be prevented by polymerase reactivation through a coupled ribosome.
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Affiliation(s)
- Liang Meng Wee
- QB3-Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA, USA
| | - Alexander B Tong
- QB3-Berkeley, Berkeley, CA, USA; Department of Chemistry, University of California Berkeley, Berkeley, CA, USA
| | - Alfredo Jose Florez Ariza
- QB3-Berkeley, Berkeley, CA, USA; Biophysics Graduate Group, University of California Berkeley, Berkeley, CA, USA
| | - Cristhian Cañari-Chumpitaz
- QB3-Berkeley, Berkeley, CA, USA; Department of Chemistry, University of California Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA, USA
| | - Patricia Grob
- QB3-Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
| | - Eva Nogales
- QB3-Berkeley, Berkeley, CA, USA; Biophysics Graduate Group, University of California Berkeley, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Carlos J Bustamante
- QB3-Berkeley, Berkeley, CA, USA; Biophysics Graduate Group, University of California Berkeley, Berkeley, CA, USA; Department of Chemistry, University of California Berkeley, Berkeley, CA, USA; Department of Physics, University of California Berkeley, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA; Kavli Energy Nanoscience Institute, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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5
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Abstract
Transcription of DNA into RNA is crucial to life, and understanding RNA polymerase (RNAP) function has received considerable attention. In contrast, how the nascent RNA folds into structures that impact transcription itself and regulate gene expression remains poorly understood. Here, we combine single-molecule Förster resonance energy transfer and site-specific fluorescent labelling of transcripts within native complexes to enable real-time cotranscriptional folding studies of a metabolite-sensing riboswitch from Escherichia coli. By monitoring the folding of riboswitches stalled at RNAP pausing sites and during active elongation, we reveal a crucial role for RNAP, which directs RNA folding to allow thiamin pyrophosphate sensing within a precise, transcriptional hotspot. Our approach offers a unique opportunity to unveil cotranscriptional processes in eukaryotic and bacterial systems. Cotranscriptional RNA folding is crucial for the timely control of biological processes, but because of its transient nature, its study has remained challenging. While single-molecule Förster resonance energy transfer (smFRET) is unique to investigate transient RNA structures, its application to cotranscriptional studies has been limited to nonnative systems lacking RNA polymerase (RNAP)–dependent features, which are crucial for gene regulation. Here, we present an approach that enables site-specific labeling and smFRET studies of kilobase-length transcripts within native bacterial complexes. By monitoring Escherichia coli nascent riboswitches, we reveal an inverse relationship between elongation speed and metabolite-sensing efficiency and show that pause sites upstream of the translation start codon delimit a sequence hotspot for metabolite sensing during transcription. Furthermore, we demonstrate a crucial role of the bacterial RNAP actively delaying the formation, within the hotspot sequence, of competing structures precluding metabolite binding. Our approach allows the investigation of cotranscriptional regulatory mechanisms in bacterial and eukaryotic elongation complexes.
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6
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Mathematical Modelling of p53 Signalling during DNA Damage Response: A Survey. Int J Mol Sci 2021; 22:ijms221910590. [PMID: 34638930 PMCID: PMC8508851 DOI: 10.3390/ijms221910590] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/14/2021] [Accepted: 09/26/2021] [Indexed: 02/05/2023] Open
Abstract
No gene has garnered more interest than p53 since its discovery over 40 years ago. In the last two decades, thanks to seminal work from Uri Alon and Ghalit Lahav, p53 has defined a truly synergistic topic in the field of mathematical biology, with a rich body of research connecting mathematic endeavour with experimental design and data. In this review we survey and distill the extensive literature of mathematical models of p53. Specifically, we focus on models which seek to reproduce the oscillatory dynamics of p53 in response to DNA damage. We review the standard modelling approaches used in the field categorising them into three types: time delay models, spatial models and coupled negative-positive feedback models, providing sample model equations and simulation results which show clear oscillatory dynamics. We discuss the interplay between mathematics and biology and show how one informs the other; the deep connections between the two disciplines has helped to develop our understanding of this complex gene and paint a picture of its dynamical response. Although yet more is to be elucidated, we offer the current state-of-the-art understanding of p53 response to DNA damage.
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7
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Turner RE, Harrison PF, Swaminathan A, Kraupner-Taylor CA, Goldie BJ, See M, Peterson AL, Schittenhelm RB, Powell DR, Creek DJ, Dichtl B, Beilharz TH. Genetic and pharmacological evidence for kinetic competition between alternative poly(A) sites in yeast. eLife 2021; 10:65331. [PMID: 34232857 PMCID: PMC8263057 DOI: 10.7554/elife.65331] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 06/22/2021] [Indexed: 01/23/2023] Open
Abstract
Most eukaryotic mRNAs accommodate alternative sites of poly(A) addition in the 3’ untranslated region in order to regulate mRNA function. Here, we present a systematic analysis of 3’ end formation factors, which revealed 3’UTR lengthening in response to a loss of the core machinery, whereas a loss of the Sen1 helicase resulted in shorter 3’UTRs. We show that the anti-cancer drug cordycepin, 3’ deoxyadenosine, caused nucleotide accumulation and the usage of distal poly(A) sites. Mycophenolic acid, a drug which reduces GTP levels and impairs RNA polymerase II (RNAP II) transcription elongation, promoted the usage of proximal sites and reversed the effects of cordycepin on alternative polyadenylation. Moreover, cordycepin-mediated usage of distal sites was associated with a permissive chromatin template and was suppressed in the presence of an rpb1 mutation, which slows RNAP II elongation rate. We propose that alternative polyadenylation is governed by temporal coordination of RNAP II transcription and 3’ end processing and controlled by the availability of 3’ end factors, nucleotide levels and chromatin landscape.
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Affiliation(s)
- Rachael Emily Turner
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
| | - Paul F Harrison
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia.,Monash Bioinformatics Platform, Monash University, Melbourne, Australia
| | - Angavai Swaminathan
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
| | - Calvin A Kraupner-Taylor
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
| | - Belinda J Goldie
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
| | - Michael See
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia.,Monash Bioinformatics Platform, Monash University, Melbourne, Australia
| | - Amanda L Peterson
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Ralf B Schittenhelm
- Monash Proteomics & Metabolomics Facility, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - David R Powell
- Monash Bioinformatics Platform, Monash University, Melbourne, Australia
| | - Darren J Creek
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Bernhard Dichtl
- School of Life and Environmental Sciences, Deakin University, Geelong, Australia
| | - Traude H Beilharz
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
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8
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Mäkinen JJ, Shin Y, Vieras E, Virta P, Metsä-Ketelä M, Murakami KS, Belogurov GA. The mechanism of the nucleo-sugar selection by multi-subunit RNA polymerases. Nat Commun 2021; 12:796. [PMID: 33542236 PMCID: PMC7862312 DOI: 10.1038/s41467-021-21005-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 01/06/2021] [Indexed: 01/18/2023] Open
Abstract
RNA polymerases (RNAPs) synthesize RNA from NTPs, whereas DNA polymerases synthesize DNA from 2'dNTPs. DNA polymerases select against NTPs by using steric gates to exclude the 2'OH, but RNAPs have to employ alternative selection strategies. In single-subunit RNAPs, a conserved Tyr residue discriminates against 2'dNTPs, whereas selectivity mechanisms of multi-subunit RNAPs remain hitherto unknown. Here, we show that a conserved Arg residue uses a two-pronged strategy to select against 2'dNTPs in multi-subunit RNAPs. The conserved Arg interacts with the 2'OH group to promote NTP binding, but selectively inhibits incorporation of 2'dNTPs by interacting with their 3'OH group to favor the catalytically-inert 2'-endo conformation of the deoxyribose moiety. This deformative action is an elegant example of an active selection against a substrate that is a substructure of the correct substrate. Our findings provide important insights into the evolutionary origins of biopolymers and the design of selective inhibitors of viral RNAPs.
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Affiliation(s)
- Janne J Mäkinen
- Department of Biochemistry, University of Turku, Turku, Finland
| | - Yeonoh Shin
- Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Eeva Vieras
- Department of Biochemistry, University of Turku, Turku, Finland
| | - Pasi Virta
- Department of Chemistry, University of Turku, Turku, Finland
| | | | - Katsuhiko S Murakami
- Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
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9
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Yu S, Li L, Cai H, He B, Gao Y, Li Y. Overexpression of NELFE contributes to gastric cancer progression via Wnt/β-catenin signaling-mediated activation of CSNK2B expression. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:54. [PMID: 33526068 PMCID: PMC7851912 DOI: 10.1186/s13046-021-01848-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 01/17/2021] [Indexed: 02/08/2023]
Abstract
Background Accumulating evidence has highlighted the importance of negative elongation factor complex member E (NELFE) in tumorigenesis. However, the relationship between NELFE and gastric cancer (GC) remains unclear. This study aimed to explore the expression pattern and specific function of NELFE in GC. Methods NELFE expression was evaluated by immunohistochemistry and qRT-PCR in GC tissues, respectively. Cell proliferation, migration and invasion were measured by CCK-8, colony formation, transwell assays, and nude mice model. Bioinformatics analysis was performed to search potential target genes of NELFE, and a Cignal Finder 10-Pathway Reporter Array was used to explore potential signaling pathways regulated by NELFE. Dual-luciferase reporter assays, qRT-PCR and western blotting were conducted to verify their regulatory relationship. The expression correlations among NELFE, β-catenin and CSNK2B were further explored by immunohistochemistry on consecutive resections. Results NELFE was significantly overexpressed in GC tissues both in protein and mRNA level and negatively correlated with the prognosis of GC patients. Gain- and loss-of-function experiments showed that NELFE potentiated GC cell proliferation and metastasis in vitro and in vivo. CSNK2B was identified as a downstream effector of NELFE. Wnt/β-catenin signaling may mediate the regulation of CSNK2B by NELFE. In addition, NELFE, β-catenin and CSNK2B were all remarkably upregulated in tumor tissues compared with adjacent normal tissues, and their expression levels in GC were positively correlated with each other. Conclusion Our findings reveal a new NELFE-Wnt/β-catenin-CSNK2B axis to promote GC progression and provide new candidate targets against this disease. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-021-01848-3.
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Affiliation(s)
- Shijun Yu
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Li Li
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Hui Cai
- Department of Geriatrics, The Second Affiliated Hospital of Zhejiang University, Hangzhou, 310009, China
| | - Bin He
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Yong Gao
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China.
| | - Yandong Li
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China.
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10
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Stringent control of the RNA-dependent RNA polymerase translocation revealed by multiple intermediate structures. Nat Commun 2020; 11:2605. [PMID: 32451382 PMCID: PMC7248106 DOI: 10.1038/s41467-020-16234-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 04/21/2020] [Indexed: 01/07/2023] Open
Abstract
Each polymerase nucleotide addition cycle is associated with two primary conformational changes of the catalytic complex: the pre-chemistry active site closure and post-chemistry translocation. While active site closure is well interpreted by numerous crystallographic snapshots, translocation intermediates are rarely captured. Here we report three types of intermediate structures in an RNA-dependent RNA polymerase (RdRP). The first two types, captured in forward and reverse translocation events, both highlight the role of RdRP-unique motif G in restricting the RNA template movement, corresponding to the rate-limiting step in translocation. By mutating two critical residues in motif G, we obtain the third type of intermediates that may mimic the transition state of this rate-limiting step, demonstrating a previously unidentified movement of the template strand. We propose that a similar strategy may be utilized by other classes of nucleic acid polymerases to ensure templating nucleotide positioning for efficient catalysis through restricting interactions with template RNA.
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11
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Belogurov GA, Artsimovitch I. The Mechanisms of Substrate Selection, Catalysis, and Translocation by the Elongating RNA Polymerase. J Mol Biol 2019; 431:3975-4006. [PMID: 31153902 DOI: 10.1016/j.jmb.2019.05.042] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 05/24/2019] [Accepted: 05/24/2019] [Indexed: 11/15/2022]
Abstract
Multi-subunit DNA-dependent RNA polymerases synthesize all classes of cellular RNAs, ranging from short regulatory transcripts to gigantic messenger RNAs. RNA polymerase has to make each RNA product in just one try, even if it takes millions of successive nucleotide addition steps. During each step, RNA polymerase selects a correct substrate, adds it to a growing chain, and moves one nucleotide forward before repeating the cycle. However, RNA synthesis is anything but monotonous: RNA polymerase frequently pauses upon encountering mechanical, chemical and torsional barriers, sometimes stepping back and cleaving off nucleotides from the growing RNA chain. A picture in which these intermittent dynamics enable processive, accurate, and controllable RNA synthesis is emerging from complementary structural, biochemical, computational, and single-molecule studies. Here, we summarize our current understanding of the mechanism and regulation of the on-pathway transcription elongation. We review the details of substrate selection, catalysis, proofreading, and translocation, focusing on rate-limiting steps, structural elements that modulate them, and accessory proteins that appear to control RNA polymerase translocation.
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Affiliation(s)
| | - Irina Artsimovitch
- Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, OH, USA.
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12
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The Role of 3' to 5' Reverse RNA Polymerization in tRNA Fidelity and Repair. Genes (Basel) 2019; 10:genes10030250. [PMID: 30917604 PMCID: PMC6471195 DOI: 10.3390/genes10030250] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 03/20/2019] [Accepted: 03/21/2019] [Indexed: 12/16/2022] Open
Abstract
The tRNAHis guanylyltransferase (Thg1) superfamily includes enzymes that are found in all three domains of life that all share the common ability to catalyze the 3′ to 5′ synthesis of nucleic acids. This catalytic activity, which is the reverse of all other known DNA and RNA polymerases, makes this enzyme family a subject of biological and mechanistic interest. Previous biochemical, structural, and genetic investigations of multiple members of this family have revealed that Thg1 enzymes use the 3′ to 5′ chemistry for multiple reactions in biology. Here, we describe the current state of knowledge regarding the catalytic features and biological functions that have been so far associated with Thg1 and its homologs. Progress toward the exciting possibility of utilizing this unusual protein activity for applications in biotechnology is also discussed.
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13
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Peck SA, Hughes KD, Victorino JF, Mosley AL. Writing a wrong: Coupled RNA polymerase II transcription and RNA quality control. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1529. [PMID: 30848101 PMCID: PMC6570551 DOI: 10.1002/wrna.1529] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 12/27/2018] [Accepted: 02/07/2019] [Indexed: 12/20/2022]
Abstract
Processing and maturation of precursor RNA species is coupled to RNA polymerase II transcription. Co-transcriptional RNA processing helps to ensure efficient and proper capping, splicing, and 3' end processing of different RNA species to help ensure quality control of the transcriptome. Many improperly processed transcripts are not exported from the nucleus, are restricted to the site of transcription, and are in some cases degraded, which helps to limit any possibility of aberrant RNA causing harm to cellular health. These critical quality control pathways are regulated by the highly dynamic protein-protein interaction network at the site of transcription. Recent work has further revealed the extent to which the processes of transcription and RNA processing and quality control are integrated, and how critically their coupling relies upon the dynamic protein interactions that take place co-transcriptionally. This review focuses specifically on the intricate balance between 3' end processing and RNA decay during transcription termination. This article is categorized under: RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms RNA Processing > 3' End Processing RNA Processing > Splicing Mechanisms RNA Processing > Capping and 5' End Modifications.
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Affiliation(s)
- Sarah A Peck
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Katlyn D Hughes
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Jose F Victorino
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Amber L Mosley
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana
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14
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Mitra P, Deshmukh AS, Gurupwar R, Kashyap P. Characterization of Toxoplasma gondii Spt5 like transcription elongation factor. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:184-197. [DOI: 10.1016/j.bbagrm.2019.01.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 12/26/2018] [Accepted: 01/06/2019] [Indexed: 12/14/2022]
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15
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Nakamura A, Wang D, Komatsu Y. Molecular mechanism of substrate recognition and specificity of tRNA His guanylyltransferase during nucleotide addition in the 3'-5' direction. RNA (NEW YORK, N.Y.) 2018; 24:1583-1593. [PMID: 30111535 PMCID: PMC6191723 DOI: 10.1261/rna.067330.118] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 08/09/2018] [Indexed: 05/06/2023]
Abstract
The tRNAHis guanylyltransferase (Thg1) transfers a guanosine triphosphate (GTP) in the 3'-5' direction onto the 5'-terminal of tRNAHis, opposite adenosine at position 73 (A73). The guanosine at the -1 position (G-1) serves as an identity element for histidyl-tRNA synthetase. To investigate the mechanism of recognition for the insertion of GTP opposite A73, first we constructed a two-stranded tRNAHis molecule composed of a primer and a template strand through division at the D-loop. Next, we evaluated the structural requirements of the incoming GTP from the incorporation efficiencies of GTP analogs into the two-piece tRNAHis Nitrogen at position 7 and the 6-keto oxygen of the guanine base were important for G-1 addition; however, interestingly, the 2-amino group was found not to be essential from the highest incorporation efficiency of inosine triphosphate. Furthermore, substitution of the conserved A73 in tRNAHis revealed that the G-1 addition reaction was more efficient onto the template containing the opposite A73 than onto the template with cytidine (C73) or other bases forming canonical Watson-Crick base-pairing. Some interaction might occur between incoming GTP and A73, which plays a role in the prevention of continuous templated 3'-5' polymerization. This study provides important insights into the mechanism of accurate tRNAHis maturation.
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Affiliation(s)
- Akiyoshi Nakamura
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo 062-8517, Japan
| | - Daole Wang
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Yasuo Komatsu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo 062-8517, Japan
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
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16
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Le TT, Wang MD. Molecular Highways—Navigating Collisions of DNA Motor Proteins. J Mol Biol 2018; 430:4513-4524. [DOI: 10.1016/j.jmb.2018.08.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 07/31/2018] [Accepted: 08/03/2018] [Indexed: 01/09/2023]
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17
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Zhang Y, Liu H, Zhou J. Oscillatory expression in Escherichia coli mediated by microRNAs with transcriptional and translational time delays. IET Syst Biol 2016; 10:203-209. [PMID: 27879474 DOI: 10.1049/iet-syb.2016.0017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The primary objective of this study is to study oscillatory expression of gene regulatory network in Escherichia coli mediated by microRNAs (sRNAs) with transcriptional and translational time delays. Motivated by the regulation of gene expression proposed by Shimoni et al. (Molecular Systems Biology, 2007), a general model of delayed gene regulatory network by sRNAs is formulated. This model can well describe many practical architectures of gene regulatory network by sRNAs, particularly when both transcriptional and translational time delays are introduced. Two functional issues on oscillatory expression of the gene regulatory network, i.e. stability and bifurcation, are investigated. Furthermore, an explicit algorithm determining the direction of Hopf bifurcation and stability of bifurcating periodic solutions is presented. It turns out that both transcriptional and translational time delays can induce gene expression in E. coli to be oscillatory even when its deterministic counterpart exhibits no oscillations. Moreover, the obtained results are in consistence with the experimental observations found in the biological literatures (Elowitz MB et al.: Nature, 2000, 403, pp. 335-338; Lennart Hilbert et al.: Mol. BioSyst, 2011, 7, pp. 2599-2607), which demonstrates that both transcriptional and translational time delays play an important role in the gene regulatory process of E. coli.
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Affiliation(s)
- Yuan Zhang
- Shanghai Key Laboratory of Mechanics in Energy Engineering, Shanghai University, Shanghai 200072, People's Republic of China
| | - Haihong Liu
- Department of Mathematics, Yunnan Normal University, Kunming 650092, People's Republic of China
| | - Jin Zhou
- Shanghai Key Laboratory of Mechanics in Energy Engineering, Shanghai University, Shanghai 200072, People's Republic of China.
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18
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Effects of σ factor competition are promoter initiation kinetics dependent. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1859:1281-8. [DOI: 10.1016/j.bbagrm.2016.07.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 07/05/2016] [Accepted: 07/07/2016] [Indexed: 01/29/2023]
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19
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Bertucat G, Lavery R, Prévost C. A Mechanism for RecA-Promoted Sequence Homology Recognition and Strand Exchange Between Single-Stranded DNA and Duplex DNA, via Triple-Helical Intermediates. J Biomol Struct Dyn 2016; 17 Suppl 1:147-53. [PMID: 22607418 DOI: 10.1080/07391102.2000.10506615] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Abstract A central function of RecA protein during homologous recombination is to promote sequence recognition and strand exchange between a stretched and unwound single-stranded DNA, to which it is complexed, and a duplex DNA. By studying the properties of DNA under the conditions of deformation imposed by RecA, we propose a model for recognition and strand exchange at the atomic level, via unusual triple-helical intermediates. In this model, association takes place within a stretched and unwound triple helix of a new type, where the invading single strand occupies the minor groove of the duplex in a parallel orientation. Our calculations indicate that strand exchange within this structure is exothermic and results in a triple helix where the third strand interacts in the major groove, the so-called R-DNA triple helix. Preliminary calculations suggest that sequence homology recognition within the triplex of association is partial and that it is completed during strand exchange and product formation.
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Affiliation(s)
- G Bertucat
- a Laboratoire de Biochimie Théorique, CNRS UPR 9080 , Institut de Biologie Physico-Chimique , 13, rue Pierre et Marie Curie , 75005 , Paris , France
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20
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Zimmer C, Häkkinen A, Ribeiro AS. Estimation of kinetic parameters of transcription from temporal single-RNA measurements. Math Biosci 2015; 271:146-53. [PMID: 26522167 DOI: 10.1016/j.mbs.2015.10.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 09/07/2015] [Accepted: 10/01/2015] [Indexed: 11/27/2022]
Abstract
Gene expression dynamics in prokaryotes is largely controlled by the multi-step process of transcription initiation whose kinetics is subject to regulation. Since the number and duration of these steps cannot be currently measured in vivo, we propose a novel method for estimating them from time series of RNA numbers in individual cells. We demonstrate the method's applicability on measurements of fluorescence-tagged RNA molecules in Escherichia coli cells, and compare with a previous method. We show that the results of the two methods agree for equal data. We also show that, when incorporating additional data, the new method produces significantly different estimates, which are in closer agreement with qPCR measurements. Unlike the previous method, the new method requires no preprocessing of the RNA numbers, using maximal information from the RNA time series. In addition, it can use data outside of the observed RNA productions. Overall, the new method characterizes the transcription initiation process with enhanced detail.
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Affiliation(s)
- Christoph Zimmer
- BIOMS, University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany.
| | - Antti Häkkinen
- Laboratory of Biosystem Dynamics, Department of Signal Processing, Tampere University of Technology, Korkeakoulunkatu 1, 33720 Tampere, Finland
| | - Andre S Ribeiro
- Laboratory of Biosystem Dynamics, Department of Signal Processing, Tampere University of Technology, Korkeakoulunkatu 1, 33720 Tampere, Finland
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21
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Arimbasseri AG, Maraia RJ. Mechanism of Transcription Termination by RNA Polymerase III Utilizes a Non-template Strand Sequence-Specific Signal Element. Mol Cell 2015; 58:1124-32. [PMID: 25959395 DOI: 10.1016/j.molcel.2015.04.002] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 03/17/2015] [Accepted: 03/30/2015] [Indexed: 01/25/2023]
Abstract
Understanding the mechanism of transcription termination by a eukaryotic RNA polymerase (RNAP) has been limited by lack of a characterizable intermediate that reflects transition from an elongation complex to a true termination event. While other multisubunit RNAPs require multipartite cis-signals and/or ancillary factors to mediate pausing and release of the nascent transcript from the clutches of these enzymes, RNAP III does so with precision and efficiency on a simple oligo(dT) tract, independent of other cis-elements or trans-factors. We report an RNAP III pre-termination complex that reveals termination mechanisms controlled by sequence-specific elements in the non-template strand. Furthermore, the TFIIF-like RNAP III subunit C37 is required for this function of the non-template strand signal. The results reveal the RNAP III terminator as an information-rich control element. While the template strand promotes destabilization via a weak oligo(rU:dA) hybrid, the non-template strand provides distinct sequence-specific destabilizing information through interactions with the C37 subunit.
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Affiliation(s)
- Aneeshkumar G Arimbasseri
- Intramural Research Program of the Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Richard J Maraia
- Intramural Research Program of the Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA; Commissioned Corps, US Public Health Service.
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22
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Productive mRNA stem loop-mediated transcriptional slippage: Crucial features in common with intrinsic terminators. Proc Natl Acad Sci U S A 2015; 112:E1984-93. [PMID: 25848054 DOI: 10.1073/pnas.1418384112] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Escherichia coli and yeast DNA-dependent RNA polymerases are shown to mediate efficient nascent transcript stem loop formation-dependent RNA-DNA hybrid realignment. The realignment was discovered on the heteropolymeric sequence T5C5 and yields transcripts lacking a C residue within a corresponding U5C4. The sequence studied is derived from a Roseiflexus insertion sequence (IS) element where the resulting transcriptional slippage is required for transposase synthesis. The stability of the RNA structure, the proximity of the stem loop to the slippage site, the length and composition of the slippage site motif, and the identity of its 3' adjacent nucleotides (nt) are crucial for transcripts lacking a single C. In many respects, the RNA structure requirements for this slippage resemble those for hairpin-dependent transcription termination. In a purified in vitro system, the slippage efficiency ranges from 5% to 75% depending on the concentration ratios of the nucleotides specified by the slippage sequence and the 3' nt context. The only previous proposal of stem loop mediated slippage, which was in Ebola virus expression, was based on incorrect data interpretation. We propose a mechanical slippage model involving the RNAP translocation state as the main motor in slippage directionality and efficiency. It is distinct from previously described models, including the one proposed for paramyxovirus, where following random movement efficiency is mainly dependent on the stability of the new realigned hybrid. In broadening the scope for utilization of transcription slippage for gene expression, the stimulatory structure provides parallels with programmed ribosomal frameshifting at the translation level.
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23
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Soultanas P. The replication-transcription conflict. Transcription 2014; 2:140-144. [PMID: 21826285 DOI: 10.4161/trns.2.3.15908] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Accepted: 04/24/2011] [Indexed: 01/21/2023] Open
Abstract
In response to environmental and nutritional stimuli, a whole array of proteins remodel genome architecture, activate or transcribe genes, suppress genes, repair lesions and base-modifications, faithfully replicate and safely separate the parental and daughter genomes during cell division. Negotiating and resolving conflicts of genome trafficking is essential for genome stability.
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Affiliation(s)
- Panos Soultanas
- Centre for Biomolecular Sciences; School of Chemistry; University Park; University of Nottingham; Nottingham, UK
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24
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Tyrosine phosphorylation of histone H2A by CK2 regulates transcriptional elongation. Nature 2014; 516:267-71. [PMID: 25252977 PMCID: PMC4461219 DOI: 10.1038/nature13736] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 08/05/2014] [Indexed: 01/08/2023]
Abstract
Post-translational histone modifications play critical roles in regulating transcription, the cell cycle, DNA replication and DNA damage repair1. The identification of new histone modifications critical for transcriptional regulation at initiation, elongation, or termination is of particular interest. Here, we report a new layer of regulation in transcriptional elongation that is conserved from yeast to mammals, based on a phosphorylation of a highly-conserved tyrosine residue, Y57, in histone H2A that is mediated by an unsuspected tyrosine kinase activity of casein kinase 2 (CK2). Mutation of H2A-Y57 in yeast or inhibition of CK2 activity impairs transcriptional elongation in yeast as well as in mammalian cells. Genome-wide binding analysis reveals that CK2α, the catalytic subunit of CK2, binds across RNA polymerase II-transcribed coding genes and active enhancers. Mutation of Y57 causes a loss of H2B mono-ubiquitylation as well as H3K4me3 and H3K79me3, histone marks associated with active transcription. Mechanistically, both CK2 inhibition and H2A-Y57F mutation enhance the H2B deubiquitylation activity of the SAGA complex, suggesting a critical role of this phosphorylation in coordinating the activity of the SAGA during transcription. Together, these results identify a new component of regulation in transcriptional elongation based on CK2-dependent tyrosine phosphorylation of the globular domain of H2A.
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25
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Kireeva ML, Kashlev M, Burton ZF. RNA polymerase structure, function, regulation, dynamics, fidelity, and roles in gene expression. Chem Rev 2014; 113:8325-30. [PMID: 24219496 DOI: 10.1021/cr400436m] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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26
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Korsnes MS, Røed SS, Tranulis MA, Espenes A, Christophersen B. Yessotoxin triggers ribotoxic stress. Toxicol In Vitro 2014; 28:975-81. [PMID: 24780217 DOI: 10.1016/j.tiv.2014.04.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2014] [Revised: 02/23/2014] [Accepted: 04/17/2014] [Indexed: 01/24/2023]
Abstract
This work tests the hypothesis that the marine algal toxin yessotoxin (YTX) can trigger ribotoxic stress response in L6 and BC3H1 myoblast cells. YTX exposure at a concentration of 100 nM displays the characteristics of a ribotoxic stress response in such cells. The exposure leads to activation of the p38 mitogen-activated protein kinase, the stress-activated protein kinase c-jun, and the double-stranded RNA-activated protein kinase (PKR). YTX treatment also causes ribosomal RNA cleavage and inhibits protein synthesis. These observations support the idea that YTX can act as a ribotoxin.
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Affiliation(s)
- Mónica Suárez Korsnes
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Campus Ås, P.O. Box 5003, NO-1432 ÅS, Norway.
| | - Susan Skogtvedt Røed
- Norwegian University of Life Sciences (NMBU), Campus Adamstuen, P.O. Box 8146, NO-0033 OSLO, Norway
| | - Michael A Tranulis
- Norwegian University of Life Sciences (NMBU), Campus Adamstuen, P.O. Box 8146, NO-0033 OSLO, Norway
| | - Arild Espenes
- Norwegian University of Life Sciences (NMBU), Campus Adamstuen, P.O. Box 8146, NO-0033 OSLO, Norway
| | - Berit Christophersen
- Norwegian University of Life Sciences (NMBU), Campus Adamstuen, P.O. Box 8146, NO-0033 OSLO, Norway
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27
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Suzuki MG, Ito H, Aoki F. Effects of RNAi-mediated knockdown of histone methyltransferases on the sex-specific mRNA expression of Imp in the silkworm Bombyx mori. Int J Mol Sci 2014; 15:6772-96. [PMID: 24758924 PMCID: PMC4013661 DOI: 10.3390/ijms15046772] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 03/25/2014] [Accepted: 04/10/2014] [Indexed: 12/11/2022] Open
Abstract
Sexual differentiation in Bombyx mori is controlled by sex-specific splicing of Bmdsx, which results in the omission of exons 3 and 4 in a male-specific manner. In B. mori, insulin-like growth factor II mRNA-binding protein (Imp) is a male-specific factor involved in male-specific splicing of Bmdsx. Male-specific Imp mRNA results from the male-specific inclusion of exon 8. To verify the link between histone methylation and alternative RNA processing in Imp, we examined the effects of RNAi-mediated knockdown of several histone methyltransferases on the sex-specific mRNA expression of Imp. As a result, male-specific expression of Imp mRNA was completely abolished when expression of the H3K79 methyltransferase DOT1L was repressed to <10% of that in control males. Chromatin immunoprecipitation-quantitative PCR analysis revealed a higher distribution of H3K79me2 in normal males than in normal females across Imp. RNA polymerase II (RNAP II) processivity assays indicated that RNAi knockdown of DOT1L in males caused a twofold decrease in RNAP II processivity compared to that in control males, with almost equivalent levels to those observed in normal females. Inhibition of RNAP II-mediated elongation in male cells repressed the male-specific splicing of Imp. Our data suggest the possibility that H3K79me2 accumulation along Imp is associated with the male-specific alternative processing of Imp mRNA that results from increased RNAP II processivity.
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Affiliation(s)
- Masataka G Suzuki
- Division of Biological Sciences, Department of Integrated Biosciences, Graduate School of Frontier Sciences, the University of Tokyo, 302 Bioscience-Bldg, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan.
| | - Haruka Ito
- Division of Biological Sciences, Department of Integrated Biosciences, Graduate School of Frontier Sciences, the University of Tokyo, 302 Bioscience-Bldg, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan.
| | - Fugaku Aoki
- Division of Biological Sciences, Department of Integrated Biosciences, Graduate School of Frontier Sciences, the University of Tokyo, 302 Bioscience-Bldg, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan.
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28
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Saraogi I, Shan SO. Co-translational protein targeting to the bacterial membrane. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1843:1433-41. [PMID: 24513458 DOI: 10.1016/j.bbamcr.2013.10.013] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2013] [Revised: 10/09/2013] [Accepted: 10/16/2013] [Indexed: 12/18/2022]
Abstract
Co-translational protein targeting by the Signal Recognition Particle (SRP) is an essential cellular pathway that couples the synthesis of nascent proteins to their proper cellular localization. The bacterial SRP, which contains the minimal ribonucleoprotein core of this universally conserved targeting machine, has served as a paradigm for understanding the molecular basis of protein localization in all cells. In this review, we highlight recent biochemical and structural insights into the molecular mechanisms by which fundamental challenges faced by protein targeting machineries are met in the SRP pathway. Collectively, these studies elucidate how an essential SRP RNA and two regulatory GTPases in the SRP and SRP receptor (SR) enable this targeting machinery to recognize, sense and respond to its biological effectors, i.e. the cargo protein, the target membrane and the translocation machinery, thus driving efficient and faithful co-translational protein targeting. This article is part of a Special Issue entitled: Protein trafficking and secretion in bacteria. Guest Editors: Anastassios Economou and Ross Dalbey.
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Affiliation(s)
- Ishu Saraogi
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
| | - Shu-ou Shan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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29
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Lin JC, Thirumalai D. Gene regulation by riboswitches with and without negative feedback loop. Biophys J 2013; 103:2320-30. [PMID: 23283231 DOI: 10.1016/j.bpj.2012.10.026] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2012] [Revised: 10/22/2012] [Accepted: 10/23/2012] [Indexed: 01/06/2023] Open
Abstract
Riboswitches, structured elements in the untranslated regions of messenger RNAs, regulate gene expression by binding specific metabolites. We introduce a kinetic network model that describes the functions of riboswitches at the systems level. Using experimental data for flavin mononucleotide riboswitch as a guide, we show that efficient function, implying a large dynamic range without compromising the requirement to suppress transcription, is determined by a balance between the transcription speed, the folding and unfolding rates of the aptamer, and the binding rates of the metabolite. We also investigated the effect of negative feedback accounting for binding to metabolites, which are themselves the products of genes that are being regulated. For a range of transcription rates negative feedback suppresses gene expression by nearly 10-fold. Negative feedback speeds the gene expression response time, and suppresses the change of steady-state protein concentration by half relative to that without feedback, when there is a modest spike in DNA concentration. A dynamic phase diagram expressed in terms of transcription speed, folding rates, and metabolite binding rates predicts different scenarios in riboswitch-mediated transcription regulation.
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Affiliation(s)
- Jong-Chin Lin
- Department of Chemistry and Biochemistry, Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, MD, USA.
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30
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Chinnappan R, Dubé A, Lemay JF, Lafontaine DA. Fluorescence monitoring of riboswitch transcription regulation using a dual molecular beacon assay. Nucleic Acids Res 2013; 41:e106. [PMID: 23525464 PMCID: PMC3664795 DOI: 10.1093/nar/gkt190] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Riboswitches are mRNA elements that specifically bind cellular metabolites and control gene expression by modifying their structure. As riboswitches often control essential genes in pathogenic bacteria, riboswitches have been proposed as new targets for antibiotics. High-throughput screening provides a powerful approach to identify riboswitch ligand analogs that could act as powerful antibacterial drugs. Biochemical assays have already been used to find riboswitch-binding analogs, but those methods do take into account the transcriptional context for riboswitch regulation. As the importance of co-transcriptional ligand binding has been shown for several riboswitches, it is vital to develop an assay that screens riboswitch-binding analogs during the transcriptional process. Here, we describe the development of a dual molecular beacon system monitoring the transcriptional regulation activity of the Bacillus subtilis pbuE adenine riboswitch. This system relies on two molecular beacons that enable the monitoring of transcription efficiency, as well as the regulatory activity of the riboswitch. Different analogs were tested using our system, and a good correlation was observed between riboswitch activity and reported metabolite affinities. This method is specific, reliable and could be applied at the high-throughput level for the identification of new potential antibiotics targeting any riboswitch-regulating gene expression at the mRNA level.
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Affiliation(s)
- Raja Chinnappan
- Department of Biology, Faculty of Sciences, RNA Group, Université de Sherbrooke, Sherbrooke, Quebec J1K 2R1, Canada
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31
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Abstract
The signal recognition particle (SRP) and its receptor compose a universally conserved and essential cellular machinery that couples the synthesis of nascent proteins to their proper membrane localization. The past decade has witnessed an explosion in in-depth mechanistic investigations of this targeting machine at increasingly higher resolutions. In this review, we summarize recent work that elucidates how the SRP and SRP receptor interact with the cargo protein and the target membrane, respectively, and how these interactions are coupled to a novel GTPase cycle in the SRP·SRP receptor complex to provide the driving force and enhance the fidelity of this fundamental cellular pathway. We also discuss emerging frontiers in which important questions remain to be addressed.
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Affiliation(s)
- David Akopian
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Kuang Shen
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Xin Zhang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Shu-ou Shan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
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32
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Intrinsic translocation barrier as an initial step in pausing by RNA polymerase II. J Mol Biol 2012; 425:697-712. [PMID: 23238253 DOI: 10.1016/j.jmb.2012.12.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Revised: 11/30/2012] [Accepted: 12/01/2012] [Indexed: 11/21/2022]
Abstract
Pausing of RNA polymerase II (RNAP II) by backtracking on DNA is a major regulatory mechanism in control of eukaryotic transcription. Backtracking occurs by extrusion of the 3' end of the RNA from the active center after bond formation and before translocation of RNAP II on DNA. In several documented cases, backtracking requires a special signal such as A/T-rich sequences forming an unstable RNA-DNA hybrid in the elongation complex. However, other sequence-dependent backtracking signals and conformations of RNAP II leading to backtracking remain unknown. Here, we demonstrate with S. cerevisiae RNAP II that a cleavage-deficient elongation factor TFIIS (TFIIS(AA)) enhances backtracked pauses during regular transcription. This is due to increased efficiency of formation of an intermediate that leads to backtracking. This intermediate may involve misalignment at the 3' end of the nascent RNA in the active center of the yeast RNAP II, and TFIIS(AA) promotes formation of this intermediate at the DNA sequences, presenting a high-energy barrier to translocation. We proposed a three-step mechanism for RNAP II pausing in which a prolonged dwell time in the pre-translocated state increases the likelihood of the 3' RNA end misalignment facilitating a backtrack pausing. These results demonstrate an important role of the intrinsic blocks to forward translocation in pausing by RNAP II.
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33
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Zhi X, Leng F. Dependence of transcription-coupled DNA supercoiling on promoter strength in Escherichia coli topoisomerase I deficient strains. Gene 2012. [PMID: 23201416 DOI: 10.1016/j.gene.2012.11.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Transcription by RNA polymerase can induce the formation of hypernegatively supercoiled DNA in vitro and in vivo. This phenomenon has been nicely explained by a "twin-supercoiled-domain" model of transcription where a positively supercoiled domain is generated ahead of the RNA polymerase and a negatively supercoiled domain behind it. In Escherichia coli topA strains, DNA gyrase selectively converts the positively supercoiled domain into negative supercoils to produce hypernegatively supercoiled DNA. In this article, in order to examine whether promoter strength affects transcription-coupled DNA supercoiling (TCDS), we developed a two-plasmid system in which a linear, non-supercoiled plasmid was used to express lac repressor constitutively while a circular plasmid was used to gage TCDS in E. coli cells. Using this two-plasmid system, we found that TCDS in topA strains is dependent on promoter strength. We also demonstrated that transcription-coupled hypernegative supercoiling of plasmid DNA did not need the expression of a membrane-insertion protein for strong promoters; however, it might require co-transcriptional synthesis of a polypeptide. Furthermore, we found that for weak promoters the expression of a membrane-insertion tet gene was not sufficient for the production of hypernegatively supercoiled DNA. Our results can be explained by the "twin-supercoiled-domain" model of transcription where the friction force applied to E. coli RNA polymerase plays a critical role in the generation of hypernegatively supercoiled DNA.
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MESH Headings
- Base Sequence
- Blotting, Western
- DNA Topoisomerases, Type I/genetics
- DNA Topoisomerases, Type I/metabolism
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Superhelical/chemistry
- DNA, Superhelical/genetics
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Escherichia coli Proteins/genetics
- Escherichia coli Proteins/metabolism
- Models, Genetic
- Molecular Sequence Data
- Mutation
- Nucleic Acid Conformation
- Plasmids/genetics
- Promoter Regions, Genetic/genetics
- Reverse Transcriptase Polymerase Chain Reaction
- Sequence Homology, Nucleic Acid
- Transcription, Genetic
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Affiliation(s)
- Xiaoduo Zhi
- Department of Chemistry & Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA
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34
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Barbi M, Mozziconacci J, Wong H, Victor JM. DNA topology in chromosomes: a quantitative survey and its physiological implications. J Math Biol 2012. [PMID: 23179130 DOI: 10.1007/s00285-012-0621-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Using a simple geometric model, we propose a general method for computing the linking number of the DNA embedded in chromatin fibers. The relevance of the method is reviewed through the single molecule experiments that have been performed in vitro with magnetic tweezers. We compute the linking number of the DNA in the manifold conformational states of the nucleosome which have been evidenced in these experiments and discuss the functional dynamics of chromosomes in the light of these manifold states.
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Affiliation(s)
- Maria Barbi
- Laboratoire de Physique Théorique de la Matière Condensée, CNRS UMR 7600, and CNRS GDR 3536, Université Pierre et Marie Curie, Case courrier 121, 4 place Jussieu, 75252 , Paris, France,
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35
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Kaplan CD. Basic mechanisms of RNA polymerase II activity and alteration of gene expression in Saccharomyces cerevisiae. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1829:39-54. [PMID: 23022618 DOI: 10.1016/j.bbagrm.2012.09.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Revised: 09/18/2012] [Accepted: 09/20/2012] [Indexed: 01/12/2023]
Abstract
Transcription by RNA polymerase II (Pol II), and all RNA polymerases for that matter, may be understood as comprising two cycles. The first cycle relates to the basic mechanism of the transcription process wherein Pol II must select the appropriate nucleoside triphosphate (NTP) substrate complementary to the DNA template, catalyze phosphodiester bond formation, and translocate to the next position on the DNA template. Performing this cycle in an iterative fashion allows the synthesis of RNA chains that can be over one million nucleotides in length in some larger eukaryotes. Overlaid upon this enzymatic cycle, transcription may be divided into another cycle of three phases: initiation, elongation, and termination. Each of these phases has a large number of associated transcription factors that function to promote or regulate the gene expression process. Complicating matters, each phase of the latter transcription cycle are coincident with cotranscriptional RNA processing events. Additionally, transcription takes place within a highly dynamic and regulated chromatin environment. This chromatin environment is radically impacted by active transcription and associated chromatin modifications and remodeling, while also functioning as a major platform for Pol II regulation. This review will focus on our basic knowledge of the Pol II transcription mechanism, and how altered Pol II activity impacts gene expression in vivo in the model eukaryote Saccharomyces cerevisiae. This article is part of a Special Issue entitled: RNA Polymerase II Transcript Elongation.
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Affiliation(s)
- Craig D Kaplan
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128, USA.
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36
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Garst AD, Porter EB, Batey RT. Insights into the regulatory landscape of the lysine riboswitch. J Mol Biol 2012; 423:17-33. [PMID: 22771573 DOI: 10.1016/j.jmb.2012.06.038] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Revised: 06/21/2012] [Accepted: 06/26/2012] [Indexed: 12/11/2022]
Abstract
A prevalent means of regulating gene expression in bacteria is by riboswitches found within mRNA leader sequences. Like protein repressors, these RNA elements must bind an effector molecule with high specificity against a background of other cellular metabolites of similar chemical structure to elicit the appropriate regulatory response. Current crystal structures of the lysine riboswitch do not provide a complete understanding of selectivity as recognition is substantially mediated through main-chain atoms of the amino acid. Using a directed set of lysine analogs and other amino acids, we have determined the relative contributions of the polar functional groups to binding affinity and the regulatory response. Our results reveal that the lysine riboswitch has >1000-fold specificity for lysine over other amino acids. The aptamer is highly sensitive to the precise placement of the ε-amino group and relatively tolerant of alterations to the main-chain functional groups in order to achieve this specificity. At low nucleotide triphosphate (NTP) concentrations, we observe good agreement between the half-maximal regulatory activity (T(50)) and the affinity of the receptor for lysine (K(d)), as well as many of its analogs. However, above 400 μM [NTP], the concentration of lysine required to elicit transcription termination rises, moving into the riboswitch into a kinetic control regime. These data demonstrate that, under physiologically relevant conditions, riboswitches can integrate both effector and NTP concentrations to generate a regulatory response appropriate for global metabolic state of the cell.
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Affiliation(s)
- Andrew D Garst
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, 596 UCB, Boulder, CO 80309-0596, USA
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37
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Zhao LN, Qin Z, Wei P, Guo HS, Dang XL, Wang SG, Tang B. Elongation factor 1β' gene from Spodoptera exigua: characterization and function identification through RNA interference. Int J Mol Sci 2012; 13:8126-8141. [PMID: 22942694 PMCID: PMC3430225 DOI: 10.3390/ijms13078126] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2012] [Revised: 06/13/2012] [Accepted: 06/18/2012] [Indexed: 01/07/2023] Open
Abstract
Elongation factor (EF) is a key regulation factor for translation in many organisms, including plants, bacteria, fungi, animals and insects. To investigate the nature and function of elongation factor 1β′ from Spodoptera exigua (SeEF-1β′), its cDNA was cloned. This contained an open reading frame of 672 nucleotides encoding a protein of 223 amino acids with a predicted molecular weight of 24.04 kDa and pI of 4.53. Northern blotting revealed that SeEF-1β′ mRNA is expressed in brain, epidermis, fat body, midgut, Malpighian tubules, ovary and tracheae. RT-PCR revealed that SeEF-1β′ mRNA is expressed at different levels in fat body and whole body during different developmental stages. In RNAi experiments, the survival rate of insects injected with SeEF-1β′ dsRNA was 58.7% at 36 h after injection, which was significantly lower than three control groups. Other elongation factors and transcription factors were also influenced when EF-1β′ was suppressed. The results demonstrate that SeEF-1β′ is a key gene in transcription in S. exigua.
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Affiliation(s)
- Li-Na Zhao
- Hangzhou Key Laboratory of Animal Adaptation and Evolution, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China; E-Mails: (L.-N.Z.); (Z.Q.); (P.W.); (H.-S.G.); (S.-G.W.)
| | - Zi Qin
- Hangzhou Key Laboratory of Animal Adaptation and Evolution, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China; E-Mails: (L.-N.Z.); (Z.Q.); (P.W.); (H.-S.G.); (S.-G.W.)
| | - Ping Wei
- Hangzhou Key Laboratory of Animal Adaptation and Evolution, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China; E-Mails: (L.-N.Z.); (Z.Q.); (P.W.); (H.-S.G.); (S.-G.W.)
| | - Hong-Shuang Guo
- Hangzhou Key Laboratory of Animal Adaptation and Evolution, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China; E-Mails: (L.-N.Z.); (Z.Q.); (P.W.); (H.-S.G.); (S.-G.W.)
| | - Xiang-Li Dang
- Zhejiang Institute of Subtropical Crops, Wenzhou, Zhejiang 325005, China; E-Mail:
| | - Shi-Gui Wang
- Hangzhou Key Laboratory of Animal Adaptation and Evolution, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China; E-Mails: (L.-N.Z.); (Z.Q.); (P.W.); (H.-S.G.); (S.-G.W.)
| | - Bin Tang
- Hangzhou Key Laboratory of Animal Adaptation and Evolution, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China; E-Mails: (L.-N.Z.); (Z.Q.); (P.W.); (H.-S.G.); (S.-G.W.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +86-571-2886-5680; Fax: +86-571-2886-5680
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38
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Muthukrishnan AB, Kandhavelu M, Lloyd-Price J, Kudasov F, Chowdhury S, Yli-Harja O, Ribeiro AS. Dynamics of transcription driven by the tetA promoter, one event at a time, in live Escherichia coli cells. Nucleic Acids Res 2012; 40:8472-83. [PMID: 22730294 PMCID: PMC3458540 DOI: 10.1093/nar/gks583] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
In Escherichia coli, tetracycline prevents translation. When subject to tetracycline, E. coli express TetA to pump it out by a mechanism that is sensitive, while fairly independent of cellular metabolism. We constructed a target gene, PtetA-mRFP1-96BS, with a 96 MS2-GFP binding site array in a single-copy BAC vector, whose expression is controlled by the tetA promoter. We measured the in vivo kinetics of production of individual RNA molecules of the target gene as a function of inducer concentration and temperature. From the distributions of intervals between transcription events, we find that RNA production by PtetA is a sub-Poissonian process. Next, we infer the number and duration of the prominent sequential steps in transcription initiation by maximum likelihood estimation. Under full induction and at optimal temperature, we observe three major steps. We find that the kinetics of RNA production under the control of PtetA, including number and duration of the steps, varies with induction strength and temperature. The results are supported by a set of logical pairwise Kolmogorov-Smirnov tests. We conclude that the expression of TetA is controlled by a sequential mechanism that is robust, whereas sensitive to external signals.
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Affiliation(s)
- Anantha-Barathi Muthukrishnan
- Laboratory of Biosystem Dynamics, Computational Systems Biology Research Group, Department of Signal Processing, Tampere University of Technology, FI-33101 Tampere, Finland
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39
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Catron B, Caruso JA, Limbach PA. Selective detection of peptide-oligonucleotide heteroconjugates utilizing capillary HPLC-ICPMS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:1053-1061. [PMID: 22451333 PMCID: PMC3348256 DOI: 10.1007/s13361-012-0366-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Revised: 12/06/2011] [Accepted: 02/18/2012] [Indexed: 05/31/2023]
Abstract
A method for the selective detection and quantification of peptide:oligonucleotide heteroconjugates, such as those generated by protein:nucleic acid cross-links, using capillary reversed-phase high performance liquid chromatography (cap-RPHPLC) coupled with inductively coupled plasma mass spectrometry detection (ICPMS) is described. The selective detection of phosphorus as (31)P(+), the only natural isotope, in peptide-oligonucleotide heteroconjugates is enabled by the elemental detection capabilities of the ICPMS. Mobile phase conditions that allow separation of heteroconjugates while maintaining ICPMS compatibility were investigated. We found that trifluoroacetic acid (TFA) mobile phases, used in conventional peptide separations, and hexafluoroisopropanol/triethylamine (HFIP/TEA) mobile phases, used in conventional oligonucleotide separations, both are compatible with ICPMS and enable heteroconjugate separation. The TFA-based separations yielded limits of detection (LOD) of ~40 ppb phosphorus, which is nearly seven times lower than the LOD for HFIP/TEA-based separations. Using the TFA mobile phase, 1-2 pmol of a model heteroconjugate were routinely separated and detected by this optimized capLC-ICPMS method.
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Affiliation(s)
- Brittany Catron
- University of Cincinnati/Agilent Technologies Metallomics Center of the Americas, Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221-0172, USA
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, P.O. Box 210172, Cincinnati, OH 45221-0172, USA
| | - Joseph A. Caruso
- University of Cincinnati/Agilent Technologies Metallomics Center of the Americas, Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221-0172, USA
| | - Patrick A. Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, P.O. Box 210172, Cincinnati, OH 45221-0172, USA
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40
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Xie P. A dynamic model for processive transcription elongation and backtracking long pauses by multisubunit RNA polymerases. Proteins 2012; 80:2020-34. [PMID: 22488837 DOI: 10.1002/prot.24090] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Revised: 03/26/2012] [Accepted: 03/30/2012] [Indexed: 11/07/2022]
Abstract
RNA polymerases are enzymes that transcribe genes from DNA onto strands of RNA. The transcription elongation by multisubunit RNA polymerases is processive but nonuniform: one enzyme can translocate along the DNA template for thousands of nucleotide addition steps but, sometimes, it can enter backtracking long pauses. Here, we present a Brownian ratchet model for the processive transcription elongation and the backtracking long pauses, which is developed based on the available structural and biochemical studies. Using the model, we analytically study the dynamics of the transcription elongation, such as the effects of external force and NTP concentration on the transcription velocity free of pauses, and the dynamics of backtracking long pauses, such as the probabilities of entering and returning from the backtracking pauses, with the analytical results in good agreement with the available single molecule experimental data. Values of several parameters for both Escherichia coli and Saccharomyces cerevisiae RNA polymerases such as their affinities for the DNA/RNA substrate during transcription elongation are determined. Moreover, some testable predictions are presented.
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Affiliation(s)
- Ping Xie
- Key Laboratory of Soft Matter Physics and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.
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41
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DNA methylation in an intron of the IBM1 histone demethylase gene stabilizes chromatin modification patterns. EMBO J 2012; 31:2981-93. [PMID: 22580822 DOI: 10.1038/emboj.2012.141] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Accepted: 04/20/2012] [Indexed: 11/09/2022] Open
Abstract
The stability of epigenetic patterns is critical for genome integrity and gene expression. This highly coordinated process involves interrelated positive and negative regulators that impact distinct epigenetic marks, including DNA methylation and dimethylation at histone H3 lysine 9 (H3K9me2). In Arabidopsis, mutations in the DNA methyltransferase MET1, which maintains CG methylation, result in aberrant patterns of other epigenetic marks, including ectopic non-CG methylation and the relocation of H3K9me2 from heterochromatin into gene-rich chromosome regions. Here, we show that the expression of the H3K9 demethylase IBM1 (increase in BONSAI methylation 1) requires DNA methylation. Surprisingly, the regulatory methylated region is contained in an unusually large intron that is conserved in IBM1 orthologues. The re-establishment of IBM1 expression in met1 mutants restored the wild-type H3K9me2 nuclear patterns, non-CG DNA methylation and transcriptional patterns at selected loci, which included DNA demethylase genes. These results provide a mechanistic explanation for long-standing puzzling observations in met1 mutants and reveal yet another layer of control in the interplay between DNA methylation and histone modification, which stabilizes DNA methylation patterns at genes.
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42
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Jackman JE, Gott JM, Gray MW. Doing it in reverse: 3'-to-5' polymerization by the Thg1 superfamily. RNA (NEW YORK, N.Y.) 2012; 18:886-99. [PMID: 22456265 PMCID: PMC3334698 DOI: 10.1261/rna.032300.112] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The tRNA(His) guanylyltransferase (Thg1) family of enzymes comprises members from all three domains of life (Eucarya, Bacteria, Archaea). Although the initial activity associated with Thg1 enzymes was a single 3'-to-5' nucleotide addition reaction that specifies tRNA(His) identity in eukaryotes, the discovery of a generalized base pair-dependent 3'-to-5' polymerase reaction greatly expanded the scope of Thg1 family-catalyzed reactions to include tRNA repair and editing activities in bacteria, archaea, and organelles. While the identification of the 3'-to-5' polymerase activity associated with Thg1 enzymes is relatively recent, the roots of this discovery and its likely physiological relevance were described ≈ 30 yr ago. Here we review recent advances toward understanding diverse Thg1 family enzyme functions and mechanisms. We also discuss possible evolutionary origins of Thg1 family-catalyzed 3'-to-5' addition activities and their implications for the currently observed phylogenetic distribution of Thg1-related enzymes in biology.
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Affiliation(s)
- Jane E Jackman
- Department of Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA.
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43
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Zhou J, Ha KS, La Porta A, Landick R, Block SM. Applied force provides insight into transcriptional pausing and its modulation by transcription factor NusA. Mol Cell 2012; 44:635-46. [PMID: 22099310 DOI: 10.1016/j.molcel.2011.09.018] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Revised: 08/22/2011] [Accepted: 09/15/2011] [Indexed: 10/15/2022]
Abstract
Transcriptional pausing by RNA polymerase (RNAP) plays an essential role in gene regulation. Pausing is modified by various elongation factors, including prokaryotic NusA, but the mechanisms underlying pausing and NusA function remain unclear. Alternative models for pausing invoke blockade events that precede translocation (on-pathway), enzyme backtracking (off-pathway), or isomerization to a nonbacktracked, elemental pause state (off-pathway). We employed an optical trapping assay to probe the motions of individual RNAP molecules transcribing a DNA template carrying tandem repeats encoding the his pause, subjecting these enzymes to controlled forces. NusA significantly decreased the pause-free elongation rate of RNAP while increasing the probability of entry into short- and long-lifetime pauses, in a manner equivalent to exerting a ~19 pN force opposing transcription. The effects of force and NusA on pause probabilities and lifetimes support a reaction scheme where nonbacktracked, elemental pauses branch off the elongation pathway from the pretranslocated state of RNAP.
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Affiliation(s)
- Jing Zhou
- Department of Applied Physics, Stanford University, Stanford, CA 94305, USA
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44
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Nakano T, Ouchi R, Kawazoe J, Pack SP, Makino K, Ide H. T7 RNA polymerases backed up by covalently trapped proteins catalyze highly error prone transcription. J Biol Chem 2012; 287:6562-72. [PMID: 22235136 DOI: 10.1074/jbc.m111.318410] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
RNA polymerases (RNAPs) transcribe genes through the barrier of nucleoproteins and site-specific DNA-binding proteins on their own or with the aid of accessory factors. Proteins are often covalently trapped on DNA by DNA damaging agents, forming DNA-protein cross-links (DPCs). However, little is known about how immobilized proteins affect transcription. To elucidate the effect of DPCs on transcription, we constructed DNA templates containing site-specific DPCs and performed in vitro transcription reactions using phage T7 RNAP. We show here that DPCs constitute strong but not absolute blocks to in vitro transcription catalyzed by T7 RNAP. More importantly, sequence analysis of transcripts shows that RNAPs roadblocked not only by DPCs but also by the stalled leading RNAP become highly error prone and generate mutations in the upstream intact template regions. This contrasts with the transcriptional mutations induced by conventional DNA lesions, which are delivered to the active site or its proximal position in RNAPs and cause direct misincorporation. Our data also indicate that the trailing RNAP stimulates forward translocation of the stalled leading RNAP, promoting the translesion bypass of DPCs. The present results provide new insights into the transcriptional fidelity and mutual interactions of RNAPs that encounter persistent roadblocks.
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Affiliation(s)
- Toshiaki Nakano
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
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45
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Development of a "modular" scheme to describe the kinetics of transcript elongation by RNA polymerase. Biophys J 2011; 101:1155-65. [PMID: 21889453 DOI: 10.1016/j.bpj.2011.07.042] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2011] [Revised: 06/20/2011] [Accepted: 07/22/2011] [Indexed: 11/22/2022] Open
Abstract
Transcript elongation by RNA polymerase involves the sequential appearance of several alternative and off-pathway states of the transcript elongation complex (TEC), and this complicates modeling of the kinetics of the transcription elongation process. Based on solutions of the chemical master equation for such transcription systems as a function of time, we here develop a modular scheme for simulating such kinetic transcription data. This scheme deals explicitly with the problem of TEC desynchronization as transcript synthesis proceeds, and develops kinetic modules to permit the various alternative states of the TECs (paused states, backtracked states, arrested states, and terminated states) to be introduced one-by-one as needed. In this way, we can set up a comprehensive kinetic model of appropriate complexity to fit the known transcriptional properties of any given DNA template and set of experimental conditions, including regulatory cofactors. In the companion article, this modular scheme is successfully used to model kinetic transcription elongation data obtained by bulk-gel electrophoresis quenching procedures and real-time surface plasmon resonance methods from a template of known sequence that contains defined pause, stall, and termination sites.
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46
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Shahravan SH, Li ITS, Truong K, Shin JA. FRep: A Fluorescent Protein-Based Bioprobe for in Vivo Detection of Protein–DNA Interactions. Anal Chem 2011; 83:9643-50. [DOI: 10.1021/ac2024602] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- S. Hesam Shahravan
- Department of Chemical and Physical Sciences, University of Toronto at Mississauga, Mississauga, Ontario, Canada L5L 1C6
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 3H6
| | - Isaac T. S. Li
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 3H6
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada M5S 3G9
| | - Kevin Truong
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada M5S 3G9
| | - Jumi A. Shin
- Department of Chemical and Physical Sciences, University of Toronto at Mississauga, Mississauga, Ontario, Canada L5L 1C6
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 3H6
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada M5S 3G9
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47
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In vivo kinetics of transcription initiation of the lar promoter in Escherichia coli. Evidence for a sequential mechanism with two rate-limiting steps. BMC SYSTEMS BIOLOGY 2011; 5:149. [PMID: 21943372 PMCID: PMC3191489 DOI: 10.1186/1752-0509-5-149] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Accepted: 09/25/2011] [Indexed: 11/10/2022]
Abstract
BACKGROUND In Escherichia coli the mean and cell-to-cell diversity in RNA numbers of different genes vary widely. This is likely due to different kinetics of transcription initiation, a complex process with multiple rate-limiting steps that affect RNA production. RESULTS We measured the in vivo kinetics of production of individual RNA molecules under the control of the lar promoter in E. coli. From the analysis of the distributions of intervals between transcription events in the regimes of weak and medium induction, we find that the process of transcription initiation of this promoter involves a sequential mechanism with two main rate-limiting steps, each lasting hundreds of seconds. Both steps become faster with increasing induction by IPTG and Arabinose. CONCLUSIONS The two rate-limiting steps in initiation are found to be important regulators of the dynamics of RNA production under the control of the lar promoter in the regimes of weak and medium induction. Variability in the intervals between consecutive RNA productions is much lower than if there was only one rate-limiting step with a duration following an exponential distribution. The methodology proposed here to analyze the in vivo dynamics of transcription may be applicable at a genome-wide scale and provide valuable insight into the dynamics of prokaryotic genetic networks.
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48
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Lemieux ME, Cheng Z, Zhou Q, White R, Cornell J, Kung AL, Rebel VI. Inactivation of a single copy of Crebbp selectively alters pre-mRNA processing in mouse hematopoietic stem cells. PLoS One 2011; 6:e24153. [PMID: 21901164 PMCID: PMC3162030 DOI: 10.1371/journal.pone.0024153] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Accepted: 08/01/2011] [Indexed: 12/15/2022] Open
Abstract
Global expression analysis of fetal liver hematopoietic stem cells (FL HSCs) revealed the presence of unspliced pre-mRNA for a number of genes in normal FL HSCs. In a subset of these genes, Crebbp+/− FL HSCs had less unprocessed pre-mRNA without a corresponding reduction in total mRNA levels. Among the genes thus identified were the key regulators of HSC function Itga4, Msi2 and Tcf4. A similar but much weaker effect was apparent in Ep300+/− FL HSCs, indicating that, in this context as in others, the two paralogs are not interchangeable. As a group, the down-regulated intronic probe sets could discriminate adult HSCs from more mature cell types, suggesting that the underlying mechanism is regulated with differentiation stage and is active in both fetal and adult hematopoiesis. Consistent with increased myelopoiesis in Crebbp hemizygous mice, targeted reduction of CREBBP abundance by shRNA in the multipotent EML cell line triggered spontaneous myeloid differentiation in the absence of the normally required inductive signals. In addition, differences in protein levels between phenotypically distinct EML subpopulations were better predicted by taking into account not only the total mRNA signal but also the amount of unspliced message present. CREBBP thus appears to selectively influence the timing and degree of pre-mRNA processing of genes essential for HSC regulation and thereby has the potential to alter subsequent cell fate decisions in HSCs.
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Affiliation(s)
- Madeleine E. Lemieux
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Ziming Cheng
- Greehey Children's Cancer Research Institute (GCCRI), The University of Texas Health Science Center at San Antonio (UTHSCSA), San Antonio, Texas, United States of America
| | - Qing Zhou
- Greehey Children's Cancer Research Institute (GCCRI), The University of Texas Health Science Center at San Antonio (UTHSCSA), San Antonio, Texas, United States of America
| | - Ruth White
- Department of Cell and Developmental Biology, Oregon Health and Science University, Portland, Oregon, United States of America
| | - John Cornell
- Department of Epidemiology and Biostatistics, The University of Texas Health Science Center at San Antonio (UTHSCSA), San Antonio, Texas, United States of America
| | - Andrew L. Kung
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Vivienne I. Rebel
- Greehey Children's Cancer Research Institute (GCCRI), The University of Texas Health Science Center at San Antonio (UTHSCSA), San Antonio, Texas, United States of America
- Department of Cellular and Structural Biology, The University of Texas Health Science Center at San Antonio (UTHSCSA), San Antonio, Texas, United States of America
- * E-mail:
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49
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Khaladkar M, Smyda M, Hannenhalli S. Epigenomic and RNA structural correlates of polyadenylation. RNA Biol 2011; 8:529-37. [PMID: 21508683 DOI: 10.4161/rna.8.3.15194] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Polyadenylation (poly(A)) of mRNA plays a critical role in regulating gene expression. Identifying the sequence, structural, and epigenomic determinants of poly(A) site usage is an important long term goal. Several cis elements that mediate poly(A) regulation have been identified. Highly used poly(A) sites are also known to have a greater nucleosome occupancy in the immediate downstream. However, a detailed exploration of additional epigenomic and mRNA structural correlates of poly(A) site usage has not been reported. Importantly, functional interaction between sequence, structure, and the epigenome in determining the poly(A) site usage is not known. We show that highly used poly(A) sites are positively associated with an mRNA structure that is energetically more favorable and one that better exposes a critical polyadenylation cis element. In exploring potential interplay between RNA and chromatin structure, we found that a stronger nucleosome occupancy downstream of poly(A) site strongly correlated with (1) a more favorable mRNA structure, and (2) a greater accumulation of RNA Polymerase II (PolII) at the poly(A) site. Further analysis suggested a causal relationship pointing from PolII accumulation to a stable RNA structure. Additionally, we found that distinct patterns of histone modifications characterize poly(A) sites and these epigenetic patterns alone can distinguish true poly(A) sites with ~76% accuracy and also discriminate between high and low usage poly(A) sites with ~74% accuracy. Our results suggest a causative link between chromatin structure and mRNA structure whereby a compacted chromatin downstream of the poly(A) site slows down the elongating transcript, thus facilitating the folding of nascent mRNA in a favorable structure at poly(A) site during transcription. Additionally we report hitherto unknown epigenomic correlates for poly(A) site usage.
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Affiliation(s)
- Mugdha Khaladkar
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
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Abstract
The signal recognition particle (SRP) is a key component of the cellular machinery that couples the ongoing synthesis of proteins to their proper localization, and has often served as a paradigm for understanding the molecular basis of protein localization within the cell. The SRP pathway exemplifies several key molecular events required for protein targeting to cellular membranes: the specific recognition of signal sequences on cargo proteins, the efficient delivery of cargo to the target membrane, the productive unloading of cargo to the translocation machinery and the precise spatial and temporal coordination of these molecular events. Here we highlight recent advances in our understanding of the molecular mechanisms underlying this pathway, and discuss new questions raised by these findings.
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Affiliation(s)
- Ishu Saraogi
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Shu-ou Shan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
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